Quantifying Spatial AMR Patterns across Urban and Rural Landscapes

Lead Research Organisation: Newcastle University
Department Name: Sch of Engineering

Abstract

Antimicrobial resistance is increasing in nature and threatens the effectiveness of our drug therapies and infection control. However, it remains difficult to distinguish what originates from human activities or what is natural. Therefore, we must extend the scale and depth monitoring efforts to better understand what is driving the increases in resistance traits.

This project will use two collections of previously characterised soils to compare and contrast distributions of AR genes under widely varying conditions, ranging from urban, agriculture, legacy mining, and pristine rural environments. The project will utilise DNA extractions and new genetic technology to quantify over 230 AR genes in the samples. Soil inventories provide us well-characterised soils and the wealth of information that describes both the soils and the impacts at source locations.

The project will generate an astonishing 120,000 AR-related data points (400 locations x 300 genes), each with extended background information on environmental conditions-creating among the largest geographic representation of AR gene distribution across landscapes ever created; sufficiently detailed to make cross-cutting observations of landscape effects on acquired vs innate AR levels. With advanced multi-parametric statistics, we will relate specific environmental conditions and factors with observed AR genes levels in soils to identify risk factors associated resistance development and impacts on human and agricultural health.

Planned Impact

"Pump prime" funding will be used to enhance and strengthen research collaborations between University of Strathclyde, Newcastle University, James Hutton Institute and the Chinese Academy of Sciences. It is also an opportunity to broaden current investigations into a holistic view of landscape-related contributions to AMR (antimicrobial resistance) in the environment. This will allow us to better understand the distributions of AMR traits, their potential sources and/or factors that affect their abundances, and contribute to geographical assessment of health risks.

The investigating team has an excellent track record of working for, and engaging with media, environmental health agencies, and the general public. To help relate results to potential health risks, we have engaged with Eleanor Anderson (Health Protection Scotland) and Prof Matt Wright (Health Protection Research Unit at Newcastle) to help interpret results in respects to public health and maximise the impact/dissemination of the information. The inclusion of these representatives will not only create opportunities to share results to those beneficiaries, but (more importantly) will allow us to keep abreast of local and regional issues and how to best carry out the research to maximise impact. Knowledge exchange is important, and meetings will be held every six months to facilitate these interactions.
Research staff and students working on this project will benefit by interacting within a multidisciplinary research team, but also through engagement with other organisations. They will gain insight not only into the technical aspects of the research, but also into the regulatory context of the work, enhancing their future employability in academia.

Publications

10 25 50
 
Description This work has shown that the international migration of antimicrobial resistance (AMR) is wider spread than previous believed. Work here has shown significant differences exist between AMR in soils in rural versus urban landscapes within the UK, but extended work has shown AMR from developed world has migrated to the HIgh Arctic. This is shown in a recent manuscript in Environment International, but then was discussed in The Conversation to explain results to the public in less technical terms. The work extended to publication in Newsweek in the US, and also is now has been included in WHO/FAO/OIE policy guidance.
Exploitation Route This has already happened and continues to happen. More will be reported as further successes are noted.
Sectors Agriculture, Food and Drink,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology

URL https://theconversation.com/antibiotic-resistant-superbug-genes-found-in-the-high-arctic-110636
 
Description A sub-element of the work performed by the NCL PDRA was published on Arctic AMR that resulted in massive media response. Three days after release over 500 unique print and web based articles were written on the work. We were then asked to write a further piece for The Conversation, which had over 20000 hits within the week and turned into a sole author story in Newsweek magazine in the US. The story continues to expand because the work only became public in 02/19. This work in conjunction with our work in Malaysia and other countries has led Graham to become at an adviser to the WHO on global WASH and AMR policy. This advisory role is expanding rapidly, including co-authoring the new WHO guidance on how to develop AMR National Action plans.
First Year Of Impact 2018
Sector Environment,Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Societal,Policy & public services

 
Description Citation to research in the US CDC and Wellcome Report on AMR
Geographic Reach Multiple continents/international 
Policy Influence Type Citation in other policy documents
URL https://wellcome.ac.uk/sites/default/files/antimicrobial-resistance-environment-report.pdf
 
Description Technical brief on water, sanitation, hygiene and wastewater management to prevent infections and reduce the spread of antimicrobial resistance. Published by World Health Organization, Food and Agriculture Organization of the United Nations, and World Organisation for Animal Health [D Graham co-author]
Geographic Reach Multiple continents/international 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
Impact This document defines the six Action Areas that need to be addressed to reduce global AMR, especially in LMICs via full WaSH implementation. The Technical Brief has been translated into six languages so far and is underpinning One Health solutions to AMR around the world.
URL https://www.who.int/publications/i/item/9789240006416
 
Description WHO/FAO/OIE Policy linking WASH Implementation and AMR Mitigation
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
Impact The policy provides evidence that implementing WASH and decentralised sanitation can reduce AMR spread in LMICs. The formal WHO/FAO/OIE Policy Brief has not yet become public (expected April 2020), but its content already has been shared with some governments and evident changes are occurring on the ground. One of the goals of the Brief is to provide a template for developing AMR National Action Plans, which was among key elements contributed by our work.
 
Description EPSRC Bright Ideas Program
Amount £251,000 (GBP)
Funding ID EP/R036705/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2020
 
Description Embedding Antimicrobial Resistance (AMR) and Childhood Malnutrition Studies in South Asia into World Health Organisation (WHO) Policy
Amount £27,033 (GBP)
Organisation Newcastle University 
Sector Academic/University
Country United Kingdom
Start 03/2020 
End 12/2020
 
Description GCRF Water Security and Sustainable Development Award
Amount £17,100,000 (GBP)
Funding ID ES/S008179/1 
Organisation Economic and Social Research Council 
Sector Public
Country United Kingdom
Start 02/2019 
End 02/2024
 
Description Impact Acceleration Award
Amount £31,000 (GBP)
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 07/2019
 
Description Newton Insititutional Award Program
Amount £80,000 (GBP)
Organisation Newton Fund 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2020
 
Description Chinese National Academy of Science - Xiamen 
Organisation Chinese Academy of Agricultural Sciences
Country China 
Sector Academic/University 
PI Contribution We are working with CAS (w/ Prof Yong-Guan Zhu) on samples from this project using our extraction methods and their multiplex qPCR methods. This is an extension of on-going joint work.
Collaborator Contribution We are sharing resistome samples for comparisons between samples within this new project, our previous collabarotion on ARC AMR, and their samples from Antartica and Tibet. The goal of this additional work is to determine how background AMR gene levels compare in "remote" locations around the world.
Impact None as of yet, but are about to submit a manuscript on AMR levels in the High Arctic.
Start Year 2012
 
Description Decentralized WASH Systems to combat Antimicrobial Resistance (AMR) workshop (Colombo, Sri Lanka) - David Graham 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This workshop was presented on behalf of the World Health Organisation. It was held at the IWA Sustainable Development Congress & Exhibition in Colombo (Sri Lanka) to inform and guide practitioners in the water industry about their critical role in reducing AMR via improved water quality. Graham, and two colleagues from IWMI (Sri Lanka) and RIVM (the Netherlands), respectively, presented the workshop, which informed the audience of future guidance from the WHO.
Year(s) Of Engagement Activity 2019
 
Description 'Superbug gene' found in one of the most remote places on earth 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Newcastle University Press Release. 28 January 2019. This release matched the storyline presented in the 29 January 2019, Antibiotic resistant 'superbug' genes found in the High Arctic, piece in The Conversation.
Year(s) Of Engagement Activity 2019
URL https://www.ncl.ac.uk/press/articles/archive/2019/01/arcticbugs/
 
Description Adviser and co-author of new WASH guidance from the World Health Organisation relative to AMR - David Graham 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact As a result of working with the US CDC, Graham was invited to advise and co-write WASH guidance. The guidance document is currently in revision (as of 02/19) with a planned publication date of 05/19. Our role was to write sections on the value of incremental sanitation improvements to reduce AMR and infectious disease. Our work was informed by all our prejects that relate environmental AMR and contaminated soils and water.
Year(s) Of Engagement Activity 2018,2019
 
Description Annual Graham Group Newsletter 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Annual Graham Research Group newsletter available online and set as a pdf to interested parties. It highlight the group's research efforts and compliments the group's research blog. It provides a condensed version for our funders, research partners, university colleagues, alumni, and students as well as friends and family.
Year(s) Of Engagement Activity 2020,2021
URL https://blogs.ncl.ac.uk/grahamr/?page_id=31
 
Description Antibiotic resistant 'superbug' genes found in the High Arctic 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact The article, presented in a layman terms, revealed the discovery of antibiotic-resistant genes in the High Artic and presented an explanation of how this finding has huge implications for global antibiotic resistance spread.
Year(s) Of Engagement Activity 2019
URL https://theconversation.com/antibiotic-resistant-superbug-genes-found-in-the-high-arctic-110636
 
Description Antimicrobial resistance in the environment of emerging countries [Amelie Ott] 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Stop-motion film entry for the Institute for Social Science Post Graduate Researcher Impact Award 2019. Awarded third place. It was posted on YouTube for 18 months but has since been made private by the creator Amelie Ott.
Year(s) Of Engagement Activity 2019
 
Description Calls for action now to prevent next global pandemic 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Newcastle University Press Office. 12 June 2020. Accouchement the accompany the Conversation piece that call for greater international co-operation to bring about improved water, sanitation and health provision as a way to prevent the next global pandemic
Year(s) Of Engagement Activity 2020
URL https://www.ncl.ac.uk/press/articles/latest/2020/06/amractionnowtopreventnextpandemic/
 
Description Co-author of the whitepaper on global led by the US Center for Disease Control - David Graham 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact The draft whitepaper was prepared for April 2, 2018. Graham was the oral spokesman on proposed whitepaper mitigation strategies related domestic and hospital waste management at the international forum in Vancouver on April 4 and 5. This event had 150 policymakers from around the world, representing over 40 countries. The final whitepaper was published in December 2018, which consolidated the Vancouver meeting and was released to the WHO and all governments that have contributed to the forum.

The report was entitled "Initiatives for Addressing Antimicrobial Resistance in the Environment: Current Situation and Challenges" and was published on the Wellcome Trust webpage. A component of the whitepaper related to rural sanitation was informed by the Newton Institutional award, using new data collected from Malaysia.
Year(s) Of Engagement Activity 2017,2018,2019
URL https://wellcome.ac.uk/sites/default/files/antimicrobial-resistance-environment-report.pdf
 
Description Expert panel and co-writer of whitepaper sponsored by the Sackler Instuitute for Nutrition and New York Academy of Science - David Graham 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Graham is working as co-author and expert advisor in developing an integrated One Health strategy for reducing antimicrobial resistance in the animal food production industry. Initial meetings are occurring now (March 2018 to March 2019) with the goal of an international launch for proposed strategies in New York in April 2019.

Launch announcement can be found at https://www.nyas.org/events/2019/antibiotics-in-animal-agriculture-what-you-need-to-know/.
Year(s) Of Engagement Activity 2018,2019
URL https://www.nyas.org/events/2019/antibiotics-in-animal-agriculture-what-you-need-to-know/
 
Description Fighting the Next Pandemic: Water quality, antimicrobial resistance, and global health 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact 2020 Newcastle University Alumni Day lecture. 10 October 2020
Year(s) Of Engagement Activity 2020
URL https://youtu.be/DB5aKt7YdD8
 
Description GrahAMR Research Group Blog 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The GrahAM Research Group blog highlights the work of the Graham research team, focusing primarily on work surrounding antimicrobial resistance (AMR), taking a collaborative and multidisciplinary approach to global health and well-being. The team of researchers, led by Newcastle University Prof David W Graham, utilises a holistic 'One Health Approach', and contributes to several of the UN's Sustainable Development Goals (SDGs).

Our research provides guidance to various international organisations, including the World Health Organisation, and bridges sustainable development, engineering, health, and sociotechnical mitigation options for reducing global AMR.

The main topics we explore are

the transmission, fate and impact of antibiotic resistance genes in the environment resulting from human activity;
energy minimization in water, wastewater and solid waste management systems;
the microbiology and ecology of greenhouse gas suppression and production in geochemical settings, especially in Polar regions; and
water and environmental quality in the developing and emerging world.
Year(s) Of Engagement Activity 2020,2021
URL https://blogs.ncl.ac.uk/grahamr/
 
Description Lecture tour of environmental and medical institutions in Israel - David Graham 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Provided a series of lectures at different organisations in Israel, including the Rambon Healthcare Center, the Technion University, The Hebrew University (in Rehovot), and at the Ben Gurian Desert Institute, all on AMR mitigation, especially blocking environmental pathways of spread. Audiences ranged from students to healthcare professionals to academics across disciplines. These have led to collaborative work on AMR spread, initially in Ethiopia. More impact would have been seen if the UK had not ceased their funding to the JPIAMR scheme.
Year(s) Of Engagement Activity 2019
 
Description Newcastle University Find Antibiotic Resistant Genes in Arctic 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Short film made available on the Newcastle University YouTube Channel. 28 January 2019. The content dovetails with the Antibiotic resistant 'superbug' genes found in the High Arctic in The Conversation and the 'Superbug gene' found in one of the most remote places on earth, Newcastle University Press Release on 28 January 2019.
Year(s) Of Engagement Activity 2019
URL https://www.youtube.com/watch?v=eDiIDkb4pDg
 
Description Policy adviser to the World Health Organisation on AMR in revised global WASH guidance 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Graham was asked and it now jointly co-writing new guidance for the World Health Organisation on AMR within new WASH policy. This guidance centres around the relative value and impact of local scale waste management technologies that can be used for reducing AMR in low resource countries. This is a central element of the Newton Institutional award; i.e., seeking such data. First reporting of information will at the WHO meeting in Ghana on November 19-20, 2018. This is meeting will be to between 100 and 200 policy representatives from over 40 countries, but the final Policy Brief will ultimately be made public, which will the report both public and global.
Year(s) Of Engagement Activity 2018,2019
 
Description Scientists around the world are already fighting the next pandemic 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Graham DW and Collignon P (9 June 2020 • 06:00 am) The Conversation.
Year(s) Of Engagement Activity 2020
URL https://theconversation.com/scientists-around-the-world-are-already-fighting-the-next-pandemic-11524...
 
Description Training Workshop on Mitigating antimicrobial Resistance (AMR) in the water cycle: Analytical methodologies and improving water quality - David Graham/David Werner 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact We organised and led this workshop in association with four universities in Ethiopia, two universities in Israel, and members of the FAO and WHO. The goal was explain AMR in comparatively simple terms, and then promote new work in Ethiopia that bridges government, NGOs and academic groups in the country. It is also taught research methods.
Year(s) Of Engagement Activity 2019
 
Description Workshop on Pharmaceuticals in the Environment: Risks in low and middle income countries (Nairobi, Kenya) - David Graham 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact This was a think tank organised by AstraZeneca to discuss the impact of pharmaceutical pollutants in the environment in developing countries. It included experts from around the world, but also included representatives from NGOs, government agencies. The product of the workshop is a call for action, which is aimed at industry and governments around the world.
Year(s) Of Engagement Activity 2019
 
Description Workshop on the use of molecular biological methods for environmental research - David Graham 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This workshop was for researchers and professional practitioners in Malaysia and Singapore. It taught how to collect environmental samples for molecular analysis, extract and purify DNA, quantify DNA signatures and then interpret data. The methods are now being using used by colleagues in Malaysia and Singapore. The course was taught by our group, but primarily by senior PhD students and junior PDRAs, both of which gained valuable experience from designing and delivering the course.
Year(s) Of Engagement Activity 2018